Microbial and autoantibody immunogenic repertoires in TIF1? autoantibody positive dermatomyositis

Spyridon Megremis; Thomas Walker; Xiaotong He; James O'Sullivan; William E.R. Ollier; Hector Chinoy; Neil Pendleton; Antony Payton; Lynne Hampson; Ian Hampson; Janine Lamb

We implemented the "Serum Antibody Repertoire Analysis (SARA)" pipeline (manuscript in preparation). SARA comprises a comprehensive workflow that integrates molecular biology peptide display and epitope signature enrichment through competitive bio-panning and high-throughput DNA next generation sequencing (NGS), alongside in-house computational scripts to reverse engineer high resolution epitope signatures that reflect original in vivo epitopes present in patient sera. SARA was applied to predict the identity and abundance of antibody epitope repertoires enriched in plasma from anti-TIF1 autoantibody-positive DM patients versus plasma from matched HC (see Supplementary Methods) . This pipeline provides a digital triage of infectious organism epitopes and autoantibodies predicted to be uniquely present or highly enriched in each sera pool. All informatics analysis was carried out using R(R Development Core Team, 2018) 3.2-3.6 and Python (Sanner, 1999) The copyright holder for this preprint (which was not peer-reviewed) is the . https://doi. org/10.1101 org/10. /2020 Separate purified Ig pools from DM and HC were used for competitive bio-panning with the FliTrxTM random 12 amino acid (AA) peptide surface display system (Lu et al., 2003) . Briefly, we first conducted a pre-panning stage to incubate separate DM and HC immobilised Ig pools with induced FliTrxTM E.